Ab initio conformational analysis of the model tripeptide N-formyl-L-alanyl-L-alanine amide
by Ramek, M.; Yu, C. H.; Schafer, L.
The ab initio conformational energy minima of the model tripeptide N-formyl-L-alanyl-L-alanine amide (ALA-ALA) were determined by ab initio RHF/4-21G and RHF/6-31G* gradient geometry refinement. For the current investigation, 11 664 RHF/4-21G structures were optimized, representing grid points in the four-dimensional (phi(1), psi(1), phi(2), psi(2)) conformational space, which were constructed in 40 degrees increments along the outer torsions phi(1) and psi(2) and in 30 degrees increments along the inner torsions psi(1) and phi(2) of ALA-ALA. Two new energy minima, previously not reported, are described. The positions of the RHF/6-31G* energy minima in phi,psi-space can differ significantly from the corresponding RHF/4-21G locations, and both sets are not clustered in the centers but on the fringes of the most populated regions of phi,psi-space in protein crystal structures. Thus, the torsion angles of the ab initio energy minima are not those of the typical substructures of proteins: the most stable helices are not alpha(R), and the torsion angles of the most stable bend forms are not those most frequently encountered in protein bends. Limitations of the dipeptide approximation are explored, illustrating how the conformational energies of an amino acid residue depend on the state of its neighbor.
- Journal
- Canadian Journal of Chemistry-Revue Canadienne de Chimie
- Volume
- 76
- Issue
- 5
- Year
- 1998
- Start Page
- 566-575
- URL
- https://dx.doi.org/10.1139/v98-063
- ISBN/ISSN
- 1480-3291; 0008-4042
- DOI
- 10.1139/v98-063